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Update 3.2 User interfaces authored by Udo Ziegler's avatar Udo Ziegler
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3-NIRVANA-user-guide/3.2-User-interfaces.md
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...@@ -820,7 +820,7 @@ for the type of coordinate system. ...@@ -820,7 +820,7 @@ for the type of coordinate system.
freely selectable parameter but computed selfconsistently from freely selectable parameter but computed selfconsistently from
the ionisation structure.* the ionisation structure.*
### Defining initial conditions ## Defining initial conditions
The user interface `configUser.c` serves to define IC for a problem. The user interface `configUser.c` serves to define IC for a problem.
Defining IC means assigning values to primary physical variables, Defining IC means assigning values to primary physical variables,
...@@ -842,8 +842,8 @@ considered primary. ...@@ -842,8 +842,8 @@ considered primary.
The mesh is represented by the master mesh pointer `gm` which is the The mesh is represented by the master mesh pointer `gm` which is the
only argument passed to function `configUser()`. The problem-relevant only argument passed to function `configUser()`. The problem-relevant
variables have to be assigned for each superblock `g` in `gm`. Recall variables have to be assigned for each superblock `g` in `gm`. Recall
the explanations about the \[mesh data the explanations about the [mesh data
structure\](3.1-Code-basics\#mesh-data-structure). structure](3.1-Code-basics\#mesh-data-structure).
There are two types of primary variables: cell-averaged variables and There are two types of primary variables: cell-averaged variables and
face-averaged variables. Cell-averaged variables are face-averaged variables. Cell-averaged variables are
...@@ -911,7 +911,7 @@ like the mass density it can be assigned at the same place. The tracer ...@@ -911,7 +911,7 @@ like the mass density it can be assigned at the same place. The tracer
array index, `ic`, runs from 0 to `_C.tracer`-1 where the code parameter array index, `ic`, runs from 0 to `_C.tracer`-1 where the code parameter
`_C.tracer` gives the number of tracers *N*<sub>*c*</sub>. Tracer `_C.tracer` gives the number of tracers *N*<sub>*c*</sub>. Tracer
variables are dimensionless and are usually defined in the range variables are dimensionless and are usually defined in the range
\[0, 1\]. \[0,1\].
Similary, species number densities, *n*<sub>*s*</sub>, are cell-averaged Similary, species number densities, *n*<sub>*s*</sub>, are cell-averaged
quantities. The species array index, `is`, runs from 0 to `_C.species`-1 quantities. The species array index, `is`, runs from 0 to `_C.species`-1
...@@ -946,6 +946,7 @@ exact integration of the analytical expressions. The so discretized ...@@ -946,6 +946,7 @@ exact integration of the analytical expressions. The so discretized
field is per se cell-wise divergence-free. For a grid cell field is per se cell-wise divergence-free. For a grid cell
(`ix`,`iy`,`iz`) on superblock `g` this means (`ix`,`iy`,`iz`) on superblock `g` this means
![ic_b](uploads/411b3e817fec94afa0a2861772697e71/ic_b.png)
$$\\mathtt{g-&gt;bx\[iz\]\[iy\]\[ix\]}=\\frac{1}{\\delta\\,\\!\\mathcal{A}\_x}\\int $$\\mathtt{g-&gt;bx\[iz\]\[iy\]\[ix\]}=\\frac{1}{\\delta\\,\\!\\mathcal{A}\_x}\\int
\\limits\_\\mathtt{g-&gt;y\[iy\]}^\\mathtt{g-&gt;y\[iy+1\]} \\limits\_\\mathtt{g-&gt;y\[iy\]}^\\mathtt{g-&gt;y\[iy+1\]}
\\int\\limits\_\\mathtt{g-&gt;z\[iz\]}^\\mathtt{g-&gt;z\[iz+1\]} B\_x(\\mathtt{g-&gt;x\[ix\]},y,z)h\_yh\_zdydz$$ \\int\\limits\_\\mathtt{g-&gt;z\[iz\]}^\\mathtt{g-&gt;z\[iz+1\]} B\_x(\\mathtt{g-&gt;x\[ix\]},y,z)h\_yh\_zdydz$$
...@@ -962,19 +963,19 @@ The numerical expressions for the cell face contents are: ...@@ -962,19 +963,19 @@ The numerical expressions for the cell face contents are:
| cell face | expression | | cell face | expression |
|:---------------------|:-----------------------------------------| |:---------------------|:-----------------------------------------|
| *δ* 𝒜<sub>*x*</sub> | `g->hyh[ix]*g->hyh[ix]*g->dvy[iy]*g->dz` | | *δ*𝒜<sub>*x*</sub> | `g->hyh[ix]*g->hyh[ix]*g->dvy[iy]*g->dz` |
| *δ* 𝒜<sub>*y*</sub> | `g->dax[ix]*g->hzyh[iy]*g->dz` | | *δ*𝒜<sub>*y*</sub> | `g->dax[ix]*g->hzyh[iy]*g->dz` |
| *δ* 𝒜<sub>*z*</sub> | `g->dax[ix]*g->dy` | | *δ*𝒜<sub>*z*</sub> | `g->dax[ix]*g->dy` |
\(2\) use of the magnetic vector potential **A**, if known, with \(2\) use of the magnetic vector potential **A**, if known, with
**B** = ∇ × **A**. When discretized in integral form this gives for the **B** = ∇ × **A**. When discretized in integral form this gives for the
face-averaged magnetic field components face-averaged magnetic field components
`g->bx[iz][iy][ix]` = \[*h*<sub>*y*</sub>*Δ*<sub>`i`*y*</sub>(*h*<sub>*z**y*</sub>*Â*<sub>*z*</sub>)−*h*<sub>*y*</sub>*Δ*<sub>`i`*z*</sub>*Â*<sub>*y*</sub>\]/*δ* 𝒜<sub>*x*</sub> `g->bx[iz][iy][ix]` = \[*h*<sub>*y*</sub>*Δ*<sub>`i`*y*</sub>(*h*<sub>*z**y*</sub>*Â*<sub>*z*</sub>)−*h*<sub>*y*</sub>*Δ*<sub>`i`*z*</sub>*Â*<sub>*y*</sub>\]/*δ*𝒜<sub>*x*</sub>
`g->by[iz][iy][ix]` = \[*Δ*<sub>`i`*z*</sub>*Â*<sub>*x*</sub>−*h*<sub>*z**y*</sub>*Δ*<sub>`i`*x*</sub>(*h*<sub>*y*</sub>*Â*<sub>*z*</sub>)\]/*δ* 𝒜<sub>*y*</sub> `g->by[iz][iy][ix]` = \[*Δ*<sub>`i`*z*</sub>*Â*<sub>*x*</sub>−*h*<sub>*z**y*</sub>*Δ*<sub>`i`*x*</sub>(*h*<sub>*y*</sub>*Â*<sub>*z*</sub>)\]/*δ*𝒜<sub>*y*</sub>
`g->bz[iz][iy][ix]` = \[*Δ*<sub>`i`*x*</sub>(*h*<sub>*y*</sub>*Â*<sub>*y*</sub>)−*Δ*<sub>`i`*y*</sub>*Â*<sub>*x*</sub>\]/*δ* 𝒜<sub>*z*</sub> `g->bz[iz][iy][ix]` = \[*Δ*<sub>`i`*x*</sub>(*h*<sub>*y*</sub>*Â*<sub>*y*</sub>)−*Δ*<sub>`i`*y*</sub>*Â*<sub>*x*</sub>\]/*δ*𝒜<sub>*z*</sub>
where (*Â*<sub>*x*</sub>, *Â*<sub>*y*</sub>, *Â*<sub>*z*</sub>) denote where (*Â*<sub>*x*</sub>, *Â*<sub>*y*</sub>, *Â*<sub>*z*</sub>) denote
the path integrals the path integrals
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